Description
CHAPTER ONE
- Introduction
1.1 Background of the study
As the germ theory of disease became established and accepted, ways were sought to turn theory into practice by studying the microbes outside the body and in turn use that information for diagnosis and treatment of human and animal disease. The industrial and scientific revolution in the late 1800’s led to wide use of microscopes to visualize microbes directly, to their classification into broad categories and to their cultivation in vitro. Once the methodologies for in vitro cultivation were standardized, it became necessary to connect the bench to the bedside.
Changes in the availability of skilled laboratory personnel, new technologies, and the financial environment willallinfluencethepracticeofdiagnosticmicrobiologyinthenearandmoredistantfuture.Becauseofthespecialexpertise needed for the accurate identification of anaerobic bacteria, the ability to diagnose anaerobic infectionsmay decline as a consequence of these changes(Abrams et al., 2015). Physicians should anticipate a difficult time in the years betweenthelossof expertisein traditionalmethodsand developmentofreliableand accuratemolecularassays.
In the future, there will be changes in the availability of skilled personnel and the prevailing economic environment will all influence clinical microbiology (Baron et al., 2012). The use of molecular-biology techniques has dramatically changed clinical microbiology and the integration of the two disciplines is an important challenge for the future. In addition to detecting well-known pathogens, the laboratories of the future will also have to be able to recognize new pathogens and participate in food-safety monitoring and bioterrorism surveillance (Benson et al., 2012). Recent experience has shown the necessity for laboratories to be able to rapidly develop diagnostic tests for new diseases that have a high social impact, as was the case with the outbreak of severe acute respiratory syndrome (SARS). Means must also be available for the rapid transfer of such technology to laboratories in which routine diagnostics are carried out. A current problem is that scientific responses to emerging threats are far more rapid than are administrative responses, and there are often prolonged delays in the approval of new diagnostic tests for use outside research laboratories.
Diagnostic microbiology is in the process of a much needed shift from conventional methods first used in 1850 to grow bacteria on culture media produced from seaweed (agar) to the molecular methods for rapid pathogen detection and identification. The molecular methods involve both genomics and proteomics in concert with bioinformatics. The FDA has now approved NAATs for multiple viruses and bacteria21. The presence of these organisms usually indicates diseases because they are not normally found on human body surfaces or tissues. Many bacteria encountered commonly in clinical practice such as Staphylococci and Escherichia coli are frequently a part of the commensal flora. It is far more challenging to interpret results showing such bacteria. Either quantitation as in the case of urinary tract infections or recovery from a normally sterile site such as blood is needed to make the detection meaningful. The technology is now being used with blood culture and for blood directly for multiple organism groups. Multiplex screenings for blood-borne viral, bacterial and protozoan parasites using an open array platform have been currently described 22. The open array platform customized with real-time PCR assays demonstrates a high level of multiplicity with sensitivity and specificity for detection of four viral, two bacterial and three protozoan blood-borne pathogens. Similar multiple real-time PCR assays are being used for detection of bacterial toxins23. A number of FDA-approved molecular diagnostic are available for rapid detection of nosocomial pathogens like MRSA, URE and Clostridium difficile24. Rapid detection of multiple antibiotic resistant genes is another recent addition to the clinical and infection transmission prevention aspects of microbiologic detection.
Several converging factors will have major impacts ondiagnostic microbiology laboratory testing in the nearfuture, defined as the next 10 years, and in the moredistant future (Abrams et al., 2015). The ideas expressed in the presentessay are opinions only, based on my own experienceand the thoughts of others in the field.
1.2 Statement of the problem
As the spectrum of microbes found to cause disease increased, it became clear that many of them have very specific growth requirements and some of the well-known pathogen have still not been cultivated in vitro, and therefore, do not fulfill the first two Koch’s postulates. The prime examples include Treponemapallidum and Mycobacterium leprae. It is important to remember that Armauer Hansen discovered Mycobacterium leprae in 1873 before Koch’s discovery of M. tuberculosis, but the inability to cultivate the leprosy bacteria in vitro allowed the credit of the germ theory to go to Koch (Renault et al., 2010).
Even with cultivable bacteria cultures fail to reveal an organism in 80% of patients with signs and symptoms consistent with an infectious process. There are multiple reasons for this under-detection including recent or current antimicrobial therapy, bacteria within biofilm especially in chronic tissue infections and device-related infections and slow growing or fastidious organisms for which necessary nutrients or cofactors for growth are not known. Even when the organism grows, it’s simply not practical to fulfill Koch’s postulates to distinguish ‘false positive’ from ‘true positive’ cultures. Both of these serious drawbacks have led to extensive empiric antibiotic use resulting in appearance of antibiotic response worldwide.
Diagnostic Microbiology is the tool that makes it possible to identify the exact etiology of infectious diseases and the most optimal therapy at the level of individual patients as well as communities. Conventional methods require time to grow the microbes in vitro under specific conditions and not all microbes are easily cultivable (Alexander et al., 2017). This is followed by biochemical methods for identification which also require hours and sometimes days. Transport of the specimens under less than ideal conditions, prior use of antibiotics and small number of organisms are among the factors that render culture-based methods less reliable. Newer methods depend on amplification of nucleic acids followed by use of probes for identification. This mitigates the need for higher microbial load, presence of metabolically active viable organisms and shortens the time to reporting. These methods can be used to detect antibiotic resistance genes directly from the specimen and help direct targeted therapy. Since these methods will not fulfill all the diagnostic needs, a second approach is being used to shorten the time to identification after the organism has already grown. Mass spectrometry and bioinformatics are the tools making this possible (Alexander et al., 2017). This study gives a review of the future of diagnostic microbiology in the next decade thereby providing means of solving problems facing diagnostic microbiology.
1.3 Justification of the study
Microbiology has never been more exciting or important than it is today. Powerful new technologies, including novel imaging techniques, genomics, proteomics, nanotechnology, rapid DNA sequencing, and massive computational capabilities have converged to make it possible for scientists to delve into inquiries that many thought would never be approachable. As a result, hardly a day goes by without another discovery that points to the central importance microbial life has in carrying out the cycles of gases and nutrients that sustain all life and affect conditions on this planet. The increasing human population, combined with increases in global travel, has apparently created a sharp rise in the emergence and re-emergence of infectious diseases, alarming the public and frustrating public health officials. This study will serve as a means of forecasting the future of diagnostic microbiology in the next decade thereby providing means of solving problems facing diagnostic microbiology.
Advancements in the study of infectious disease, microbial ecology, plant and animal pathology, and biotechnology promise to improve human life and the well-being of the environment, and new opportunities have come about through social and scientific changes.
1.4 Research Question
This study will provide answers to the following question:
- But in what direction is microbial science going?
- What will best improve people’s lives and the health through diagnostic microbiology?
- What new directions should microbiology take in the next decade?
1.5 Scope of the study
This study covers knowing the changing in the wake of advancements in technology and growing human pressures on the world’s resources.
1.6 Significance of the study
This study will serve as a means of knowing how microbial science is changing in the wake of advancements in technology and growing human pressures on the world’s resources.
This study will serve as a means of knowing if the topic deserves exploration and where the obstacles to exploring those areas lie. As we stand at the convergence of genomics, public concerns about bioterrorism, global outbreaks of infectious diseases, unprecedented computational power, and the possibility of large-scale ecological disasters.
